Egypt's Coptic minority is celebrating its first Christmas under Islamist rule and amid a climate of fear and uncertainty for their future, although President Mohammed Morsi has pledged to be the "president of all Egyptians."

In September, residents and officials reported that several Coptic families from Rafah had fled from the Sinai peninsula town that borders the Gaza Strip after receiving death threats from Islamists.

Egyptian security sources suggested, meanwhile, that the planned attack could have been aimed at a military camp under construction near the church which has been targeted in the past by Islamist militants.

They said the church has been lying abandoned for the past two years after it was torched in the aftermath of the countrywide uprising that toppled the regime of former President Hosni Mubarak in February 2011.

It was not immediately clear who was behind the planned attack but one security source said the perpetrators were "probably radical Islamists whom security forces have been tracking for months."

Morsi, who hails from the powerful Muslim Brotherhood, visited the Sinai peninsula in October to meet with and reassure Coptic families, telling them that "your security is our security".

Egypt's Copts, who make up six to 10 per cent of the country's population of 83 million, have regularly complained of discrimination and marginalisation and have also been the target of numerous sectarian attacks.

One of the worst incidents of violence occurred on January 1, 2011 when 23 people were killed in an attack on a Coptic church in the Mediterranean city of Alexandria.

Sinai, a scarcely populated peninsula home to lucrative tourist resorts in the south and shadowy Islamist militants in the north, is a major transit point for arms smuggling to Gaza which is ruled by the Islamist Hamas group.

Security in the desert and mountainous region collapsed after the uprising that toppled Mubarak.

Since his downfall, several militant attacks have targeted police and soldiers, including a brazen August 5 ambush on an army outpost that killed 16 soldiers.

The military launched a wide-ranging campaign after that attack to flush out militants, but drive-by shootings have continued.

And on Friday security officials announced the seizure in Sinai of US-made anti-tank and surface-to-air missiles destined for Gaza, where militants have said they would acquire more weapons to use against Israel.